"Flores had a little bit of right shoulder tendinitis," manager Dan Jennings said. "We'll go with Narveson in that spot."
Miami has not yet determined if Flores will be headed to the disabled list.
Flores, a promising rookie right-hander, made his first big league start last Friday, and he worked five innings, giving up five runs on seven hits, while throwing 85 pitches.
The 23-year-old, acquired from the Giants last December for Casey McGehee, has also made six relief appearances. He opened the season at Double-A Jacksonville, and moved up to Triple-A New Orleans.
In 2014, the Marlins used 13 different starters, which is a franchise high for a season.
The Marlins currently have starters Jose Fernandez, Henderson Alvarez, Jarred Cosart and Jose Urena on the disabled list. Alvarez is out for the season after undergoing shoulder surgery. Fernandez, Cosart and Urena are expected back in September.
Narveson, 33, has made six relief appearances since being called up from New Orleans. The veteran last started in the big leagues with the Brewers in 2012.
The left-hander has dealt with injuries in recent years, dealing with a torn rotator cuff in 2012.